From b8f0f3fdd298f0cec08f45c58bbb6800538c6a46 Mon Sep 17 00:00:00 2001 From: Ron Levine Date: Wed, 26 Nov 2014 15:59:02 -0500 Subject: [PATCH] Add argument for loading the vector HMM library once --- .../haplotypecaller/HaplotypeCaller.java | 77 +++++++++++++------ .../PairHMMLikelihoodCalculationEngine.java | 9 ++- .../utils/pairhmm/DebugJNILoglessPairHMM.java | 4 +- .../utils/pairhmm/VectorLoglessPairHMM.java | 7 +- ...LikelihoodCalculationEnginesBenchmark.java | 2 +- ...lexAndSymbolicVariantsIntegrationTest.java | 9 ++- .../HaplotypeCallerGVCFIntegrationTest.java | 53 ++++++------- .../HaplotypeCallerIntegrationTest.java | 54 ++++++------- .../HaplotypeCallerModesIntegrationTest.java | 3 +- ...aplotypeCallerParallelIntegrationTest.java | 3 +- ...MMLikelihoodCalculationEngineUnitTest.java | 2 +- ...ngLikelihoodCalculationEngineUnitTest.java | 2 +- 12 files changed, 132 insertions(+), 93 deletions(-) diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeCaller.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeCaller.java index c48889d37..2f1b4ba3b 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeCaller.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeCaller.java @@ -109,7 +109,7 @@ import java.io.PrintStream; import java.util.*; /** - * Call SNPs and indels simultaneously via local re-assembly of haplotypes in an active region. + * Call SNPs and indels simultaneously via local re-assembly of haplotypes in an active region * *

The basic operation of the HaplotypeCaller proceeds as follows:

* @@ -140,6 +140,7 @@ import java.util.*; * read data to calculate the likelihoods of each genotype per sample given the read data observed for that * sample. The most likely genotype is then assigned to the sample.

* + * *
*

Input

*

@@ -148,7 +149,10 @@ import java.util.*; * *

Output

*

- * VCF file with raw, unfiltered SNP and indel calls. These must be filtered either by variant recalibration (best) or hard-filtering before use in downstream analyses. + * VCF file with raw, unfiltered SNP and indel calls. These must be filtered either by variant recalibration (best) + * or hard-filtering before use in downstream analyses. If using the reference-confidence model workflow for cohort + * analysis, the output is a GVCF file that must first be run through GenotypeGVCFs and then filtering before further + * analysis. *

* *

Examples

@@ -158,7 +162,7 @@ import java.util.*; * Best Practices documentation for detailed recommendations.

* *
- *

Single-sample all-sites calling on DNAseq (for GVCF-based cohort analysis workflow)

+ *

Single-sample all-sites calling on DNAseq (for `-ERC GVCF` cohort analysis workflow)

*

* 

  *   java
@@ -210,11 +214,19 @@ import java.util.*;
  * 
Caveats

  * 
  *
+ * 
Additional Notes

+ * 
+ *
  */
 
 @DocumentedGATKFeature( groupName = HelpConstants.DOCS_CAT_VARDISC, extraDocs = {CommandLineGATK.class} )
@@ -237,12 +249,12 @@ public class HaplotypeCaller extends ActiveRegionWalker, In
     @Hidden
     @Advanced
     @Argument(fullName="likelihoodCalculationEngine",shortName="likelihoodEngine",
-            doc="what likelihood calculation engine to use to calculate the relative likelihood of reads vs haplotypes",required=false)
+            doc="What likelihood calculation engine to use to calculate the relative likelihood of reads vs haplotypes",required=false)
     protected ReadLikelihoodCalculationEngine.Implementation likelihoodEngineImplementation = ReadLikelihoodCalculationEngine.Implementation.PairHMM;
 
     @Hidden
     @Advanced
-    @Argument(fullName="heterogeneousKmerSizeResolution",shortName="hksr",doc="how to solve heterogeneous kmer situations using the fast method",required=false)
+    @Argument(fullName="heterogeneousKmerSizeResolution",shortName="hksr",doc="How to solve heterogeneous kmer situations using the fast method",required=false)
     protected HeterogeneousKmerSizeResolution heterogeneousKmerSizeResolution = HeterogeneousKmerSizeResolution.COMBO_MIN;
 
     /**
@@ -258,22 +270,22 @@ public class HaplotypeCaller extends ActiveRegionWalker, In
      * Turning on this mode may result in serious performance cost for the HC.  It's really only appropriate to
      * use in specific areas where you want to better understand why the HC is making specific calls.
      *
-     * The reads are written out containing a HC tag (integer) that encodes which haplotype each read best matches
+     * The reads are written out containing an "HC" tag (integer) that encodes which haplotype each read best matches
      * according to the haplotype caller's likelihood calculation.  The use of this tag is primarily intended
-     * to allow good coloring of reads in IGV.  Simply go to Color Alignments By > Tag and enter HC to more
+     * to allow good coloring of reads in IGV.  Simply go to "Color Alignments By > Tag" and enter "HC" to more
      * easily see which reads go with these haplotype.
      *
      * Note that the haplotypes (called or all, depending on mode) are emitted as single reads covering the entire
      * active region, coming from read HC and a special read group.
      *
-     * Note that only reads that are actually informative about the haplotypes are emitted.  By informative we mean
+     * Note also that only reads that are actually informative about the haplotypes are emitted.  By informative we mean
      * that there's a meaningful difference in the likelihood of the read coming from one haplotype compared to
      * its next best haplotype.
      *
      * The best way to visualize the output of this mode is with IGV.  Tell IGV to color the alignments by tag,
      * and give it the HC tag, so you can see which reads support each haplotype.  Finally, you can tell IGV
-     * to group by sample, which will separate the potential haplotypes from the reads.  All of this can be seen
-     * in the following screenshot: https://www.dropbox.com/s/xvy7sbxpf13x5bp/haplotypecaller%20bamout%20for%20docs.png
+     * to group by sample, which will separate the potential haplotypes from the reads.  All of this can be seen in
+     * this screenshot
      *
      */
     @Advanced
@@ -286,7 +298,7 @@ public class HaplotypeCaller extends ActiveRegionWalker, In
      * considered (top 128 max) or just the ones that were selected as alleles and assigned to samples.
      */
     @Advanced
-    @Argument(fullName="bamWriterType", shortName="bamWriterType", doc="Which haplotypes should be written to the BAM?", required = false)
+    @Argument(fullName="bamWriterType", shortName="bamWriterType", doc="Which haplotypes should be written to the BAM", required = false)
     public HaplotypeBAMWriter.Type bamWriterType = HaplotypeBAMWriter.Type.CALLED_HAPLOTYPES;
 
     /**
@@ -322,7 +334,7 @@ public class HaplotypeCaller extends ActiveRegionWalker, In
      * filtered in the comp track will be ignored. Note that 'dbSNP' has been special-cased (see the --dbsnp argument).
      */
     @Advanced
-    @Input(fullName="comp", shortName = "comp", doc="comparison VCF file", required=false)
+    @Input(fullName="comp", shortName = "comp", doc="Comparison VCF file", required=false)
     public List> comps = Collections.emptyList();
     public List> getCompRodBindings() { return comps; }
 
@@ -332,7 +344,8 @@ public class HaplotypeCaller extends ActiveRegionWalker, In
     public boolean alwaysAppendDbsnpId() { return false; }
 
     /**
-     * Which annotations to add to the output VCF file. The single value 'none' removes the default annotations. See the VariantAnnotator -list argument to view available annotations.
+     * Which annotations to add to the output VCF file. The single value 'none' removes the default annotations.
+     * See the VariantAnnotator -list argument to view available annotations.
      */
     @Advanced
     @Argument(fullName="annotation", shortName="A", doc="One or more specific annotations to apply to variant calls", required=false)
@@ -491,11 +504,10 @@ public class HaplotypeCaller extends ActiveRegionWalker, In
     protected int gcpHMM = 10;
 
     /**
-     * If this flag is provided, the haplotype caller will include unmapped reads (that have chromosomal coordinates) in the assembly and calling
-     * when these reads occur in the region being analyzed.  Typically, for paired end analyses, one pair of the
-     * read can map, but if its pair is too divergent then it may be unmapped and placed next to its mate, taking
-     * the mates contig and alignment start.  If this flag is provided the haplotype caller will see such reads,
-     * and may make use of them in assembly and calling, where possible.
+     * If this flag is provided, the HaplotypeCaller will include unmapped reads (that have chromosomal coordinates) in the assembly and calling
+     * when these reads occur in the region being analyzed.  This situation can occur in paired end analyses, when one read in the read pair
+     * gets mapped but its mate is too divergent. In that case, the mate will be marked as unmapped and placed next to the first read, assigned to the same
+     * contig and alignment start.  If this flag is provided, the HaplotypeCaller will see such reads, and may make use of them in assembly and calling, where possible.
      */
     @Hidden
     @Argument(fullName="includeUmappedReads", shortName="unmapped", doc="Include unmapped reads with chromosomal coordinates", required = false)
@@ -538,10 +550,10 @@ public class HaplotypeCaller extends ActiveRegionWalker, In
     protected boolean mergeVariantsViaLD = false;
 
     /**
-     * As of GATK 3.3, HaplotypeCaller outputs physical information (see release notes and documentation for details). This argument disables that behavior.
+     * As of GATK 3.3, HaplotypeCaller outputs physical (read-based) information (see version 3.3 release notes and documentation for details). This argument disables that behavior.
      */
     @Advanced
-    @Argument(fullName="doNotRunPhysicalPhasing", shortName="doNotRunPhysicalPhasing", doc="Don't try to add physical (read-based) phasing information", required = false)
+    @Argument(fullName="doNotRunPhysicalPhasing", shortName="doNotRunPhysicalPhasing", doc="Disable physical phasing", required = false)
     protected boolean doNotRunPhysicalPhasing = false;
 
     public static final String HAPLOTYPE_CALLER_PHASING_ID_KEY = "PID";
@@ -557,13 +569,30 @@ public class HaplotypeCaller extends ActiveRegionWalker, In
     @Argument(fullName = "pair_hmm_implementation", shortName = "pairHMM", doc = "The PairHMM implementation to use for genotype likelihood calculations", required = false)
     public PairHMM.HMM_IMPLEMENTATION pairHMM = PairHMM.HMM_IMPLEMENTATION.VECTOR_LOGLESS_CACHING;
 
+    /**
+     * This argument is intended for use in the test suite only. It gives developers the ability to select of the
+     * hardware dependent vectorized implementation of the vectorized PairHMM library (pairHMM=VECTOR_LOGLESS_CACHING).
+     * For normal usage, you should rely on the architecture auto-detection.
+     */
     @Hidden
     @Advanced
-    @Argument(fullName = "pair_hmm_sub_implementation", shortName = "pairHMMSub", doc = "The PairHMM machine dependent sub-implementation to use for genotype likelihood calculations. Usage is intended for test suite use only, normal usage you should rely on the architecture auto-detection", required = false)
+    @Argument(fullName = "pair_hmm_sub_implementation", shortName = "pairHMMSub", doc = "The PairHMM machine-dependent sub-implementation to use for genotype likelihood calculations", required = false)
     public PairHMM.HMM_SUB_IMPLEMENTATION pairHMMSub = PairHMM.HMM_SUB_IMPLEMENTATION.ENABLE_ALL;
 
+    /**
+     * This argument is intended for use in the test suite only. It gives developers the ability to load different
+     * hardware dependent sub-implementations (-pairHMMSub) of the vectorized PairHMM library (-pairHMM=VECTOR_LOGLESS_CACHING)
+     * for each test. Without this option, the library is only loaded once (for the first test executed in the suite) even if
+     * subsequent tests specify a different implementation.
+     * Each test will output the corresponding library loading messages.
+     */
     @Hidden
-    @Argument(fullName="keepRG", shortName="keepRG", doc="Only use read from this read group when making calls (but use all reads to build the assembly)", required = false)
+    @Advanced
+    @Argument(fullName = "always_load_vector_logless_PairHMM_lib", shortName = "alwaysloadVectorHMM", doc = "Load the vector logless PairHMM library each time a GATK run is initiated in the test suite", required = false)
+    public boolean alwaysLoadVectorLoglessPairHMMLib = false;
+
+    @Hidden
+    @Argument(fullName="keepRG", shortName="keepRG", doc="Only use reads from this read group when making calls (but use all reads to build the assembly)", required = false)
     protected String keepRG = null;
 
     /**
@@ -892,7 +921,7 @@ public class HaplotypeCaller extends ActiveRegionWalker, In
     private ReadLikelihoodCalculationEngine createLikelihoodCalculationEngine() {
         switch (likelihoodEngineImplementation) {
             case PairHMM:
-                return new PairHMMLikelihoodCalculationEngine( (byte)gcpHMM, pairHMM, pairHMMSub, log10GlobalReadMismappingRate, noFpga, pcrErrorModel );
+                return new PairHMMLikelihoodCalculationEngine( (byte)gcpHMM, pairHMM, pairHMMSub, alwaysLoadVectorLoglessPairHMMLib, log10GlobalReadMismappingRate, noFpga, pcrErrorModel );
             case GraphBased:
                 return new GraphBasedLikelihoodCalculationEngine( (byte)gcpHMM,log10GlobalReadMismappingRate, heterogeneousKmerSizeResolution,SCAC.DEBUG,debugGraphTransformations);
             case Random:
diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/PairHMMLikelihoodCalculationEngine.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/PairHMMLikelihoodCalculationEngine.java
index c7aac0c1d..7b2a5647c 100644
--- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/PairHMMLikelihoodCalculationEngine.java
+++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/PairHMMLikelihoodCalculationEngine.java
@@ -84,6 +84,7 @@ public class PairHMMLikelihoodCalculationEngine implements ReadLikelihoodCalcula
 
     private final PairHMM.HMM_IMPLEMENTATION hmmType;
     private final PairHMM.HMM_SUB_IMPLEMENTATION hmmSubType;
+    private final boolean alwaysLoadVectorLoglessPairHMMLib;
     private final boolean noFpga;
 
     private final ThreadLocal pairHMMThreadLocal = new ThreadLocal() {
@@ -100,7 +101,7 @@ public class PairHMMLikelihoodCalculationEngine implements ReadLikelihoodCalcula
                 case VECTOR_LOGLESS_CACHING:
                     try
                     {
-                        return new VectorLoglessPairHMM(hmmSubType);
+                        return new VectorLoglessPairHMM(hmmSubType, alwaysLoadVectorLoglessPairHMMLib);
                     }
                     catch(UnsatisfiedLinkError ule)
                     {
@@ -108,7 +109,7 @@ public class PairHMMLikelihoodCalculationEngine implements ReadLikelihoodCalcula
                         return new LoglessPairHMM();
                     }
                 case DEBUG_VECTOR_LOGLESS_CACHING:
-                    return new DebugJNILoglessPairHMM(PairHMM.HMM_IMPLEMENTATION.VECTOR_LOGLESS_CACHING, hmmSubType);
+                    return new DebugJNILoglessPairHMM(PairHMM.HMM_IMPLEMENTATION.VECTOR_LOGLESS_CACHING, hmmSubType, alwaysLoadVectorLoglessPairHMMLib);
                 case ARRAY_LOGLESS:
                     if (noFpga || !CnyPairHMM.isAvailable())
                         return new ArrayLoglessPairHMM();
@@ -150,6 +151,7 @@ public class PairHMMLikelihoodCalculationEngine implements ReadLikelihoodCalcula
      * @param constantGCP the gap continuation penalty to use with the PairHMM
      * @param hmmType the type of the HMM to use
      * @param hmmSubType the type of the machine dependent sub-implementation of HMM to use
+     * @param alwaysLoadVectorLoglessPairHMMLib always load the vector logless HMM library instead of once
      * @param log10globalReadMismappingRate the global mismapping probability, in log10(prob) units.  A value of
      *                                      -3 means that the chance that a read doesn't actually belong at this
      *                                      location in the genome is 1 in 1000.  The effect of this parameter is
@@ -162,9 +164,10 @@ public class PairHMMLikelihoodCalculationEngine implements ReadLikelihoodCalcula
      * @param pcrErrorModel model to correct for PCR indel artifacts
      */
     public PairHMMLikelihoodCalculationEngine( final byte constantGCP, final PairHMM.HMM_IMPLEMENTATION hmmType, final PairHMM.HMM_SUB_IMPLEMENTATION hmmSubType,
-                                               final double log10globalReadMismappingRate, final boolean noFpga, final PCR_ERROR_MODEL pcrErrorModel ) {
+                                               final boolean alwaysLoadVectorLoglessPairHMMLib, final double log10globalReadMismappingRate, final boolean noFpga, final PCR_ERROR_MODEL pcrErrorModel ) {
         this.hmmType = hmmType;
         this.hmmSubType = hmmSubType;
+        this.alwaysLoadVectorLoglessPairHMMLib = alwaysLoadVectorLoglessPairHMMLib;
         this.constantGCP = constantGCP;
         this.log10globalReadMismappingRate = log10globalReadMismappingRate;
         this.noFpga = noFpga;
diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/utils/pairhmm/DebugJNILoglessPairHMM.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/utils/pairhmm/DebugJNILoglessPairHMM.java
index fd2adb9dd..eaaf1798f 100644
--- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/utils/pairhmm/DebugJNILoglessPairHMM.java
+++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/utils/pairhmm/DebugJNILoglessPairHMM.java
@@ -92,11 +92,11 @@ public class DebugJNILoglessPairHMM extends LoglessPairHMM {
     protected HashMap filenameToWriter = new HashMap();
 
     private JNILoglessPairHMM jniPairHMM = null;
-    public DebugJNILoglessPairHMM(final PairHMM.HMM_IMPLEMENTATION hmmType, PairHMM.HMM_SUB_IMPLEMENTATION pairHMMSub) {
+    public DebugJNILoglessPairHMM(final PairHMM.HMM_IMPLEMENTATION hmmType, PairHMM.HMM_SUB_IMPLEMENTATION pairHMMSub, final boolean alwaysLoadVectorLoglessPairHMMLib) {
         super();
         switch(hmmType) {
             case VECTOR_LOGLESS_CACHING:
-                jniPairHMM = new VectorLoglessPairHMM(pairHMMSub);
+                jniPairHMM = new VectorLoglessPairHMM(pairHMMSub, alwaysLoadVectorLoglessPairHMMLib);
                 break;
             default:
                 throw new UserException.BadArgumentValue("pairHMM","Specified JNIPairHMM implementation is unrecognized or incompatible with the HaplotypeCaller. Acceptable options are VECTOR_LOGLESS_CACHING");
diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/utils/pairhmm/VectorLoglessPairHMM.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/utils/pairhmm/VectorLoglessPairHMM.java
index 2bc2d135c..896c07d18 100644
--- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/utils/pairhmm/VectorLoglessPairHMM.java
+++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/utils/pairhmm/VectorLoglessPairHMM.java
@@ -107,7 +107,7 @@ public class VectorLoglessPairHMM extends JNILoglessPairHMM {
     private static Boolean isVectorLoglessPairHMMLibraryLoaded = false;
 
     //The constructor is called only once inside PairHMMLikelihoodCalculationEngine
-    public VectorLoglessPairHMM(PairHMM.HMM_SUB_IMPLEMENTATION pairHMMSub) throws UserException.HardwareFeatureException {
+    public VectorLoglessPairHMM(final PairHMM.HMM_SUB_IMPLEMENTATION pairHMMSub, final boolean alwaysLoadVectorLoglessPairHMMLib) throws UserException.HardwareFeatureException {
         super();
 
         synchronized (isVectorLoglessPairHMMLibraryLoaded) {
@@ -116,8 +116,9 @@ public class VectorLoglessPairHMM extends JNILoglessPairHMM {
             long mask = pairHMMSub.getMask();
             throwIfHardwareFeatureNotSupported(mask, pairHMMSub);
 
-            //Load the library and initialize the FieldIDs
-            if (!isVectorLoglessPairHMMLibraryLoaded) {
+            // Load the library and initialize the FieldIDs
+            // Load if not loaded or if the the always load flag is true
+            if (!isVectorLoglessPairHMMLibraryLoaded || alwaysLoadVectorLoglessPairHMMLib) {
                 try
                 {
                     //Try loading from Java's library path first
diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HCLikelihoodCalculationEnginesBenchmark.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HCLikelihoodCalculationEnginesBenchmark.java
index 01f12d4e4..c46a2a2de 100644
--- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HCLikelihoodCalculationEnginesBenchmark.java
+++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HCLikelihoodCalculationEnginesBenchmark.java
@@ -126,7 +126,7 @@ public class HCLikelihoodCalculationEnginesBenchmark extends SimpleBenchmark {
     public void timeLoglessPairHMM(final int reps) {
         for (int i = 0; i < reps; i++) {
             final PairHMMLikelihoodCalculationEngine engine = new PairHMMLikelihoodCalculationEngine((byte) 10,
-                    PairHMM.HMM_IMPLEMENTATION.LOGLESS_CACHING, PairHMM.HMM_SUB_IMPLEMENTATION.ENABLE_ALL,-3, true, PairHMMLikelihoodCalculationEngine.PCR_ERROR_MODEL.NONE);
+                    PairHMM.HMM_IMPLEMENTATION.LOGLESS_CACHING, PairHMM.HMM_SUB_IMPLEMENTATION.UNVECTORIZED, true, -3, true, PairHMMLikelihoodCalculationEngine.PCR_ERROR_MODEL.NONE);
             engine.computeReadLikelihoods(dataSet.assemblyResultSet(), SampleListUtils.singletonList("anonymous"), Collections.singletonMap("anonymous", dataSet.readList()));
         }
     }
diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeCallerComplexAndSymbolicVariantsIntegrationTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeCallerComplexAndSymbolicVariantsIntegrationTest.java
index cbb9abcc2..45c486d1e 100644
--- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeCallerComplexAndSymbolicVariantsIntegrationTest.java
+++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeCallerComplexAndSymbolicVariantsIntegrationTest.java
@@ -62,9 +62,10 @@ import static org.broadinstitute.gatk.tools.walkers.haplotypecaller.HaplotypeCal
 public class HaplotypeCallerComplexAndSymbolicVariantsIntegrationTest extends WalkerTest {
 
     final static String HMM_SUB_IMPLEMENTATION = "UNVECTORIZED";
+    final static String ALWAYS_LOAD_VECTOR_HMM = "-alwaysloadVectorHMM";
 
     private void HCTestComplexVariants(String bam, String args, String md5) {
-        final String base = String.format("-T HaplotypeCaller --contamination_fraction_to_filter 0.05 --disableDithering --pcr_indel_model NONE -pairHMMSub %s -R %s -I %s", HMM_SUB_IMPLEMENTATION, REF, bam) + " -L 20:10028767-10028967 -L 20:10431524-10431924 -L 20:10723661-10724061 -L 20:10903555-10903955 --no_cmdline_in_header -o %s -minPruning 4";
+        final String base = String.format("-T HaplotypeCaller --contamination_fraction_to_filter 0.05 --disableDithering --pcr_indel_model NONE -pairHMMSub %s %s -R %s -I %s", HMM_SUB_IMPLEMENTATION, ALWAYS_LOAD_VECTOR_HMM, REF, bam) + " -L 20:10028767-10028967 -L 20:10431524-10431924 -L 20:10723661-10724061 -L 20:10903555-10903955 --no_cmdline_in_header -o %s -minPruning 4";
         final WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(base + " " + args, Arrays.asList(md5));
         executeTest("testHaplotypeCallerComplexVariants: args=" + args, spec);
     }
@@ -75,7 +76,7 @@ public class HaplotypeCallerComplexAndSymbolicVariantsIntegrationTest extends Wa
     }
 
     private void HCTestSymbolicVariants(String bam, String args, String md5) {
-        final String base = String.format("-T HaplotypeCaller --disableDithering --pcr_indel_model NONE -pairHMMSub %s -R %s -I %s", HMM_SUB_IMPLEMENTATION, REF, bam) + " -L 20:5947969-5948369 -L 20:61091236-61091636 --no_cmdline_in_header -o %s -minPruning 1";
+        final String base = String.format("-T HaplotypeCaller --disableDithering --pcr_indel_model NONE -pairHMMSub %s %s -R %s -I %s", HMM_SUB_IMPLEMENTATION, ALWAYS_LOAD_VECTOR_HMM, REF, bam) + " -L 20:5947969-5948369 -L 20:61091236-61091636 --no_cmdline_in_header -o %s -minPruning 1";
         final WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(base + " " + args, Arrays.asList(md5));
         executeTest("testHaplotypeCallerSymbolicVariants: args=" + args, spec);
     }
@@ -87,7 +88,7 @@ public class HaplotypeCallerComplexAndSymbolicVariantsIntegrationTest extends Wa
     }
 
     private void HCTestComplexGGA(String bam, String args, String md5) {
-        final String base = String.format("-T HaplotypeCaller --disableDithering --pcr_indel_model NONE -pairHMMSub %s -R %s -I %s", HMM_SUB_IMPLEMENTATION, REF, bam) + " --no_cmdline_in_header -o %s -minPruning 3 -gt_mode GENOTYPE_GIVEN_ALLELES -alleles " + validationDataLocation + "combined.phase1.chr20.raw.indels.sites.vcf";
+        final String base = String.format("-T HaplotypeCaller --disableDithering --pcr_indel_model NONE -pairHMMSub %s %s -R %s -I %s", HMM_SUB_IMPLEMENTATION, ALWAYS_LOAD_VECTOR_HMM, REF, bam) + " --no_cmdline_in_header -o %s -minPruning 3 -gt_mode GENOTYPE_GIVEN_ALLELES -alleles " + validationDataLocation + "combined.phase1.chr20.raw.indels.sites.vcf";
         final WalkerTestSpec spec = new WalkerTestSpec(base + " " + args, Arrays.asList(md5));
         executeTest("testHaplotypeCallerComplexGGA: args=" + args, spec);
     }
@@ -105,7 +106,7 @@ public class HaplotypeCallerComplexAndSymbolicVariantsIntegrationTest extends Wa
     }
 
     private void HCTestComplexConsensusMode(String bam, String args, String md5) {
-        final String base = String.format("-T HaplotypeCaller --disableDithering --pcr_indel_model NONE -pairHMMSub %s -R %s -I %s", HMM_SUB_IMPLEMENTATION, REF, bam) + " --no_cmdline_in_header -o %s -consensus -alleles " + validationDataLocation + "combined.phase1.chr20.raw.indels.sites.vcf -alleles " + validationDataLocation + "phase1.projectConsensus.chr20.raw.snps.vcf";
+        final String base = String.format("-T HaplotypeCaller --disableDithering --pcr_indel_model NONE -pairHMMSub %s %s -R %s -I %s", HMM_SUB_IMPLEMENTATION, ALWAYS_LOAD_VECTOR_HMM, REF, bam) + " --no_cmdline_in_header -o %s -consensus -alleles " + validationDataLocation + "combined.phase1.chr20.raw.indels.sites.vcf -alleles " + validationDataLocation + "phase1.projectConsensus.chr20.raw.snps.vcf";
         final WalkerTestSpec spec = new WalkerTestSpec(base + " " + args, Arrays.asList(md5));
         executeTest("testHaplotypeCallerComplexConsensusMode: args=" + args, spec);
     }
diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeCallerGVCFIntegrationTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeCallerGVCFIntegrationTest.java
index eb2bf5db0..a666b3dea 100644
--- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeCallerGVCFIntegrationTest.java
+++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeCallerGVCFIntegrationTest.java
@@ -64,6 +64,7 @@ import java.util.List;
 public class HaplotypeCallerGVCFIntegrationTest extends WalkerTest {
 
     final static String HMM_SUB_IMPLEMENTATION = "UNVECTORIZED";
+    final static String ALWAYS_LOAD_VECTOR_HMM = "-alwaysloadVectorHMM";
 
     @DataProvider(name = "MyDataProviderHaploid")
     public Object[][] makeMyDataProviderHaploid() {
@@ -96,9 +97,9 @@ public class HaplotypeCallerGVCFIntegrationTest extends WalkerTest {
         tests.add(new Object[]{NA12878_PCRFREE, ReferenceConfidenceMode.BP_RESOLUTION, PCRFreeIntervals, "f38178834961798d79e7190dbca004bf"});
         tests.add(new Object[]{NA12878_PCRFREE, ReferenceConfidenceMode.GVCF, PCRFreeIntervals, "762dde6b938dd7bb988f132dd9e4b76f"});
         tests.add(new Object[]{NA12878_WEx, ReferenceConfidenceMode.NONE, WExIntervals, "1c3570461e96ad6d66c6abb0fd6ee865"});
-        tests.add(new Object[]{NA12878_WEx, ReferenceConfidenceMode.BP_RESOLUTION, WExIntervals, "66019a0914f905522da6bd3b557a57d1"});
+        tests.add(new Object[]{NA12878_WEx, ReferenceConfidenceMode.BP_RESOLUTION, WExIntervals, "2a5a7057faba3cd488e40186072156af"});
 
-        final String NA12878bandedResolutionMD5 = "de763f6c9a5aec4586a2671941e4c96d";
+        final String NA12878bandedResolutionMD5 = "a7ca9f08d94ece61799f5083ff4227cc";
         tests.add(new Object[]{NA12878_WEx, ReferenceConfidenceMode.GVCF, WExIntervals, NA12878bandedResolutionMD5});
         tests.add(new Object[]{NA12878_WEx + " -I " + privateTestDir + "NA20313.highCoverageRegion.bam -sn NA12878",
                 ReferenceConfidenceMode.GVCF, WExIntervals, NA12878bandedResolutionMD5});
@@ -119,8 +120,8 @@ public class HaplotypeCallerGVCFIntegrationTest extends WalkerTest {
         tests.add(new Object[]{NA12878_PCRFREE, ReferenceConfidenceMode.BP_RESOLUTION, PCRFreeIntervals, "3f9e2b721c3bc8a6d76aa75bb7544f28"});
         tests.add(new Object[]{NA12878_PCRFREE, ReferenceConfidenceMode.GVCF, PCRFreeIntervals, "dac179dc0c314e2ac7e39ecb9d334493"});
         tests.add(new Object[]{NA12878_WEx, ReferenceConfidenceMode.NONE, WExIntervals, "eac793500fbc7de46259000dbbcdd27d"});
-        tests.add(new Object[]{NA12878_WEx, ReferenceConfidenceMode.BP_RESOLUTION, WExIntervals, "4a431e0e387de3f791318f67d8855b0b"});
-        tests.add(new Object[]{NA12878_WEx, ReferenceConfidenceMode.GVCF, WExIntervals, "1058d3fe6553e07f002f994759c9647d"});
+        tests.add(new Object[]{NA12878_WEx, ReferenceConfidenceMode.BP_RESOLUTION, WExIntervals, "dc1b8abd195b75e147ac78fdbd4e2b65"});
+        tests.add(new Object[]{NA12878_WEx, ReferenceConfidenceMode.GVCF, WExIntervals, "b4d75b53ce85fbaaad949a087c3ec86b"});
 
         return tests.toArray(new Object[][]{});
     }
@@ -130,8 +131,8 @@ public class HaplotypeCallerGVCFIntegrationTest extends WalkerTest {
      */
     @Test(dataProvider = "MyDataProvider")
     public void testHCWithGVCF(String bam, ReferenceConfidenceMode mode, String intervals, String md5) {
-        final String commandLine = String.format("-T HaplotypeCaller --disableDithering --pcr_indel_model NONE -pairHMMSub %s -R %s -I %s %s -ERC %s --no_cmdline_in_header -variant_index_type %s -variant_index_parameter %d",
-                HMM_SUB_IMPLEMENTATION, b37KGReference, bam, intervals, mode, HaplotypeCaller.OPTIMAL_GVCF_INDEX_TYPE, HaplotypeCaller.OPTIMAL_GVCF_INDEX_PARAMETER);
+        final String commandLine = String.format("-T HaplotypeCaller --disableDithering --pcr_indel_model NONE -pairHMMSub %s %s -R %s -I %s %s -ERC %s --no_cmdline_in_header -variant_index_type %s -variant_index_parameter %d",
+                HMM_SUB_IMPLEMENTATION, ALWAYS_LOAD_VECTOR_HMM, b37KGReference, bam, intervals, mode, HaplotypeCaller.OPTIMAL_GVCF_INDEX_TYPE, HaplotypeCaller.OPTIMAL_GVCF_INDEX_PARAMETER);
         final String name = "testHCWithGVCF bam=" + bam + " intervals= " + intervals + " gvcf= " + mode;
         final WalkerTestSpec spec = new WalkerTestSpec(commandLine + " -o %s", Arrays.asList(md5));
         executeTest(name, spec);
@@ -142,8 +143,8 @@ public class HaplotypeCallerGVCFIntegrationTest extends WalkerTest {
      */
     @Test(dataProvider = "MyDataProviderHaploid", enabled=true)
     public void testHCWithGVCFHaploid(final String bam, final ReferenceConfidenceMode mode, final String intervals, final String md5) {
-        final String commandLine = String.format("-T HaplotypeCaller -ploidy 1 --disableDithering --pcr_indel_model NONE -pairHMMSub %s -R %s -I %s %s -ERC %s --no_cmdline_in_header -variant_index_type %s -variant_index_parameter %d",
-                HMM_SUB_IMPLEMENTATION, b37KGReference, bam, intervals, mode, HaplotypeCaller.OPTIMAL_GVCF_INDEX_TYPE, HaplotypeCaller.OPTIMAL_GVCF_INDEX_PARAMETER);
+        final String commandLine = String.format("-T HaplotypeCaller -ploidy 1 --disableDithering --pcr_indel_model NONE -pairHMMSub %s %s -R %s -I %s %s -ERC %s --no_cmdline_in_header -variant_index_type %s -variant_index_parameter %d",
+                HMM_SUB_IMPLEMENTATION, ALWAYS_LOAD_VECTOR_HMM, b37KGReference, bam, intervals, mode, HaplotypeCaller.OPTIMAL_GVCF_INDEX_TYPE, HaplotypeCaller.OPTIMAL_GVCF_INDEX_PARAMETER);
         final String name = "testHCWithGVCFHaploid bam=" + bam + " intervals= " + intervals + " gvcf= " + mode;
         final WalkerTestSpec spec = new WalkerTestSpec(commandLine + " -o %s", Arrays.asList(md5));
         executeTest(name, spec);
@@ -154,8 +155,8 @@ public class HaplotypeCallerGVCFIntegrationTest extends WalkerTest {
      */
     @Test(dataProvider = "MyDataProviderTetraploid", enabled=true)
     public void testHCWithGVCFTetraploid(final String bam, final ReferenceConfidenceMode mode, final String intervals, final String md5) {
-        final String commandLine = String.format("-T HaplotypeCaller -ploidy 4 --disableDithering --pcr_indel_model NONE -pairHMMSub %s -R %s -I %s %s -ERC %s --no_cmdline_in_header -variant_index_type %s -variant_index_parameter %d",
-                HMM_SUB_IMPLEMENTATION, b37KGReference, bam, intervals, mode, HaplotypeCaller.OPTIMAL_GVCF_INDEX_TYPE, HaplotypeCaller.OPTIMAL_GVCF_INDEX_PARAMETER);
+        final String commandLine = String.format("-T HaplotypeCaller -ploidy 4 --disableDithering --pcr_indel_model NONE -pairHMMSub %s %s -R %s -I %s %s -ERC %s --no_cmdline_in_header -variant_index_type %s -variant_index_parameter %d",
+                HMM_SUB_IMPLEMENTATION, ALWAYS_LOAD_VECTOR_HMM, b37KGReference, bam, intervals, mode, HaplotypeCaller.OPTIMAL_GVCF_INDEX_TYPE, HaplotypeCaller.OPTIMAL_GVCF_INDEX_PARAMETER);
         final String name = "testHCWithGVCFTetraploid bam=" + bam + " intervals= " + intervals + " gvcf= " + mode;
         final WalkerTestSpec spec = new WalkerTestSpec(commandLine + " -o %s", Arrays.asList(md5));
         executeTest(name, spec);
@@ -163,8 +164,8 @@ public class HaplotypeCallerGVCFIntegrationTest extends WalkerTest {
 
     @Test
     public void testERCRegionWithNoCalledHaplotypes() {
-        final String commandLine = String.format("-T HaplotypeCaller --pcr_indel_model NONE -pairHMMSub %s -R %s -I %s -L %s -ERC GVCF -variant_index_type %s -variant_index_parameter %d",
-                HMM_SUB_IMPLEMENTATION, b37KGReference, privateTestDir + "noCallRefModel.bam", "20:17000001-18000001", HaplotypeCaller.OPTIMAL_GVCF_INDEX_TYPE, HaplotypeCaller.OPTIMAL_GVCF_INDEX_PARAMETER);
+        final String commandLine = String.format("-T HaplotypeCaller --pcr_indel_model NONE -pairHMMSub %s %s -R %s -I %s -L %s -ERC GVCF -variant_index_type %s -variant_index_parameter %d",
+                HMM_SUB_IMPLEMENTATION, ALWAYS_LOAD_VECTOR_HMM, b37KGReference, privateTestDir + "noCallRefModel.bam", "20:17000001-18000001", HaplotypeCaller.OPTIMAL_GVCF_INDEX_TYPE, HaplotypeCaller.OPTIMAL_GVCF_INDEX_PARAMETER);
         final WalkerTestSpec spec = new WalkerTestSpec(commandLine + " -o %s", Arrays.asList(""));
         spec.disableShadowBCF();
         executeTest("testERCRegionWithNoCalledHaplotypes", spec);
@@ -172,8 +173,8 @@ public class HaplotypeCallerGVCFIntegrationTest extends WalkerTest {
 
     @Test()
     public void testMissingGVCFIndexException() {
-        final String commandLine = String.format("-T HaplotypeCaller --pcr_indel_model NONE -pairHMMSub %s -R %s -I %s -L %s -ERC GVCF",
-                HMM_SUB_IMPLEMENTATION, b37KGReference, privateTestDir + "noCallRefModel.bam", "20:17000001-18000001");
+        final String commandLine = String.format("-T HaplotypeCaller --pcr_indel_model NONE -pairHMMSub %s %s -R %s -I %s -L %s -ERC GVCF",
+                HMM_SUB_IMPLEMENTATION, ALWAYS_LOAD_VECTOR_HMM, b37KGReference, privateTestDir + "noCallRefModel.bam", "20:17000001-18000001");
         final WalkerTestSpec spec = new WalkerTestSpec(commandLine + " -o %s", 1, UserException.GVCFIndexException.class);
         spec.disableShadowBCF();
         executeTest("testMissingGVCFIndexingStrategyException", spec);
@@ -181,8 +182,8 @@ public class HaplotypeCallerGVCFIntegrationTest extends WalkerTest {
 
     @Test()
     public void testWrongParameterGVCFIndexException() {
-        final String commandLine = String.format("-T HaplotypeCaller --pcr_indel_model NONE -pairHMMSub %s -R %s -I %s -L %s -ERC GVCF -variant_index_type %s -variant_index_parameter %d",
-                HMM_SUB_IMPLEMENTATION, b37KGReference, privateTestDir + "noCallRefModel.bam", "20:17000001-18000001", HaplotypeCaller.OPTIMAL_GVCF_INDEX_TYPE, HaplotypeCaller.OPTIMAL_GVCF_INDEX_PARAMETER + 1);
+        final String commandLine = String.format("-T HaplotypeCaller --pcr_indel_model NONE -pairHMMSub %s %s -R %s -I %s -L %s -ERC GVCF -variant_index_type %s -variant_index_parameter %d",
+                HMM_SUB_IMPLEMENTATION, ALWAYS_LOAD_VECTOR_HMM, b37KGReference, privateTestDir + "noCallRefModel.bam", "20:17000001-18000001", HaplotypeCaller.OPTIMAL_GVCF_INDEX_TYPE, HaplotypeCaller.OPTIMAL_GVCF_INDEX_PARAMETER + 1);
         final WalkerTestSpec spec = new WalkerTestSpec(commandLine + " -o %s", 1, UserException.GVCFIndexException.class);
         spec.disableShadowBCF();
         executeTest("testMissingGVCFIndexingStrategyException", spec);
@@ -195,8 +196,8 @@ public class HaplotypeCallerGVCFIntegrationTest extends WalkerTest {
         if (HaplotypeCaller.OPTIMAL_GVCF_INDEX_TYPE == GATKVCFIndexType.DYNAMIC_SEEK)
             type = GATKVCFIndexType.DYNAMIC_SIZE;
 
-        final String commandLine = String.format("-T HaplotypeCaller --pcr_indel_model NONE -pairHMMSub %s -R %s -I %s -L %s -ERC GVCF -variant_index_type %s -variant_index_parameter %d",
-                HMM_SUB_IMPLEMENTATION, b37KGReference, privateTestDir + "noCallRefModel.bam", "20:17000001-18000001", type, HaplotypeCaller.OPTIMAL_GVCF_INDEX_PARAMETER);
+        final String commandLine = String.format("-T HaplotypeCaller --pcr_indel_model NONE -pairHMMSub %s %s -R %s -I %s -L %s -ERC GVCF -variant_index_type %s -variant_index_parameter %d",
+                HMM_SUB_IMPLEMENTATION, ALWAYS_LOAD_VECTOR_HMM, b37KGReference, privateTestDir + "noCallRefModel.bam", "20:17000001-18000001", type, HaplotypeCaller.OPTIMAL_GVCF_INDEX_PARAMETER);
         final WalkerTestSpec spec = new WalkerTestSpec(commandLine + " -o %s", 1, UserException.GVCFIndexException.class);
         spec.disableShadowBCF();
         executeTest("testMissingGVCFIndexingStrategyException", spec);
@@ -207,8 +208,8 @@ public class HaplotypeCallerGVCFIntegrationTest extends WalkerTest {
 
     @Test()
     public void testWrongGVCFNonVariantRecordOrderBugFix() {
-        final String commandLine = String.format("-T HaplotypeCaller --pcr_indel_model NONE -pairHMMSub %s -R %s -I %s -L %s -ERC GVCF --no_cmdline_in_header -variant_index_type %s -variant_index_parameter %d",
-                HMM_SUB_IMPLEMENTATION, b37KGReference, WRONG_GVCF_RECORD_ORDER_BUGFIX_BAM, WRONG_GVCF_RECORD_ORDER_BUGFIX_INTERVALS, HaplotypeCaller.OPTIMAL_GVCF_INDEX_TYPE, HaplotypeCaller.OPTIMAL_GVCF_INDEX_PARAMETER);
+        final String commandLine = String.format("-T HaplotypeCaller --pcr_indel_model NONE -pairHMMSub %s %s -R %s -I %s -L %s -ERC GVCF --no_cmdline_in_header -variant_index_type %s -variant_index_parameter %d",
+                HMM_SUB_IMPLEMENTATION, ALWAYS_LOAD_VECTOR_HMM, b37KGReference, WRONG_GVCF_RECORD_ORDER_BUGFIX_BAM, WRONG_GVCF_RECORD_ORDER_BUGFIX_INTERVALS, HaplotypeCaller.OPTIMAL_GVCF_INDEX_TYPE, HaplotypeCaller.OPTIMAL_GVCF_INDEX_PARAMETER);
         final WalkerTestSpec spec = new WalkerTestSpec(commandLine + " -o %s", Arrays.asList("e6a4e571abb59b925d59a38d244f0abe"));
         spec.disableShadowBCF();
         executeTest("testMissingGVCFIndexingStrategyException", spec);
@@ -224,8 +225,8 @@ public class HaplotypeCallerGVCFIntegrationTest extends WalkerTest {
 
     @Test
     public void testNoCallGVCFMissingPLsBugFix() {
-        final String commandLine = String.format("-T HaplotypeCaller --pcr_indel_model NONE -pairHMMSub %s -R %s -I %s -L %s -ERC GVCF --no_cmdline_in_header -variant_index_type %s -variant_index_parameter %d",
-                HMM_SUB_IMPLEMENTATION, b37KGReference, NOCALL_GVCF_BUGFIX_BAM, NOCALL_GVCF_BUGFIX_INTERVALS, HaplotypeCaller.OPTIMAL_GVCF_INDEX_TYPE, HaplotypeCaller.OPTIMAL_GVCF_INDEX_PARAMETER);
+        final String commandLine = String.format("-T HaplotypeCaller --pcr_indel_model NONE -pairHMMSub %s %s -R %s -I %s -L %s -ERC GVCF --no_cmdline_in_header -variant_index_type %s -variant_index_parameter %d",
+                HMM_SUB_IMPLEMENTATION, ALWAYS_LOAD_VECTOR_HMM, b37KGReference, NOCALL_GVCF_BUGFIX_BAM, NOCALL_GVCF_BUGFIX_INTERVALS, HaplotypeCaller.OPTIMAL_GVCF_INDEX_TYPE, HaplotypeCaller.OPTIMAL_GVCF_INDEX_PARAMETER);
         final WalkerTestSpec spec = new WalkerTestSpec(commandLine + " -o %s", Arrays.asList("7ef1f30d92178f75e5220b16508b47cd"));
         spec.disableShadowBCF();
         executeTest("testNoCallGVCFMissingPLsBugFix", spec);
@@ -236,8 +237,8 @@ public class HaplotypeCallerGVCFIntegrationTest extends WalkerTest {
      */
     @Test(enabled=true)
     public void testGeneralPloidyArrayIndexBug1Fix() {
-        final String commandLine = String.format("-T HaplotypeCaller --pcr_indel_model NONE -pairHMMSub %s -R %s -I %s -L %s -ERC GVCF --no_cmdline_in_header -variant_index_type %s -variant_index_parameter %d -ploidy 1 -maxAltAlleles 2 -isr INTERSECTION -L 1:23696115-23696189",
-                HMM_SUB_IMPLEMENTATION, b37KGReference, GENERAL_PLOIDY_BUGFIX1_BAM, GENERAL_PLOIDY_BUGFIX1_INTERVALS, HaplotypeCaller.OPTIMAL_GVCF_INDEX_TYPE, HaplotypeCaller.OPTIMAL_GVCF_INDEX_PARAMETER);
+        final String commandLine = String.format("-T HaplotypeCaller --pcr_indel_model NONE -pairHMMSub %s %s -R %s -I %s -L %s -ERC GVCF --no_cmdline_in_header -variant_index_type %s -variant_index_parameter %d -ploidy 1 -maxAltAlleles 2 -isr INTERSECTION -L 1:23696115-23696189",
+                HMM_SUB_IMPLEMENTATION, ALWAYS_LOAD_VECTOR_HMM, b37KGReference, GENERAL_PLOIDY_BUGFIX1_BAM, GENERAL_PLOIDY_BUGFIX1_INTERVALS, HaplotypeCaller.OPTIMAL_GVCF_INDEX_TYPE, HaplotypeCaller.OPTIMAL_GVCF_INDEX_PARAMETER);
         final WalkerTestSpec spec = new WalkerTestSpec(commandLine + " -o %s", Arrays.asList(""));
         spec.disableShadowBCF();
         executeTest(" testGeneralPloidyArrayIndexBug1Fix", spec);
@@ -248,8 +249,8 @@ public class HaplotypeCallerGVCFIntegrationTest extends WalkerTest {
      */
     @Test(enabled=true)
     public void testGeneralPloidyArrayIndexBug2Fix() {
-        final String commandLine = String.format("-T HaplotypeCaller --pcr_indel_model NONE -pairHMMSub %s -R %s -I %s -L %s -ERC GVCF --no_cmdline_in_header -variant_index_type %s -variant_index_parameter %d -ploidy 2 -maxAltAlleles 2 -A DepthPerSampleHC -A StrandBiasBySample -L 1:38052860-38052937",
-                HMM_SUB_IMPLEMENTATION, b37KGReference, GENERAL_PLOIDY_BUGFIX2_BAM, GENERAL_PLOIDY_BUGFIX2_INTERVALS, HaplotypeCaller.OPTIMAL_GVCF_INDEX_TYPE, HaplotypeCaller.OPTIMAL_GVCF_INDEX_PARAMETER);
+        final String commandLine = String.format("-T HaplotypeCaller --pcr_indel_model NONE -pairHMMSub %s %s -R %s -I %s -L %s -ERC GVCF --no_cmdline_in_header -variant_index_type %s -variant_index_parameter %d -ploidy 2 -maxAltAlleles 2 -A DepthPerSampleHC -A StrandBiasBySample -L 1:38052860-38052937",
+                HMM_SUB_IMPLEMENTATION, ALWAYS_LOAD_VECTOR_HMM, b37KGReference, GENERAL_PLOIDY_BUGFIX2_BAM, GENERAL_PLOIDY_BUGFIX2_INTERVALS, HaplotypeCaller.OPTIMAL_GVCF_INDEX_TYPE, HaplotypeCaller.OPTIMAL_GVCF_INDEX_PARAMETER);
         final WalkerTestSpec spec = new WalkerTestSpec(commandLine + " -o %s", Arrays.asList(""));
         spec.disableShadowBCF();
         executeTest(" testGeneralPloidyArrayIndexBug2Fix", spec);
diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeCallerIntegrationTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeCallerIntegrationTest.java
index 6d57aeff6..f72cf4e6f 100644
--- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeCallerIntegrationTest.java
+++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeCallerIntegrationTest.java
@@ -83,9 +83,10 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest {
     final static String INTERVALS_FILE = validationDataLocation + "NA12878.HiSeq.b37.chr20.10_11mb.test.intervals";
     final static String GGA_INTERVALS_FILE = privateTestDir + "haplotype-caller-reduced-test-interval.list";
     final static String HMM_SUB_IMPLEMENTATION = "UNVECTORIZED";
+    final static String ALWAYS_LOAD_VECTOR_HMM = "-alwaysloadVectorHMM";
 
     private void HCTest(String bam, String args, String md5) {
-        final String base = String.format("-T HaplotypeCaller --contamination_fraction_to_filter 0.05 --disableDithering --pcr_indel_model NONE --maxReadsInRegionPerSample 1000 --minReadsPerAlignmentStart 5 --maxProbPropagationDistance 50 --activeProbabilityThreshold 0.002 -pairHMMSub %s -R %s -I %s -L %s", HMM_SUB_IMPLEMENTATION, REF, bam, INTERVALS_FILE) + " --no_cmdline_in_header -o %s -minPruning 3";
+        final String base = String.format("-T HaplotypeCaller --contamination_fraction_to_filter 0.05 --disableDithering --pcr_indel_model NONE --maxReadsInRegionPerSample 1000 --minReadsPerAlignmentStart 5 --maxProbPropagationDistance 50 --activeProbabilityThreshold 0.002 -pairHMMSub %s %s -R %s -I %s -L %s", HMM_SUB_IMPLEMENTATION, ALWAYS_LOAD_VECTOR_HMM, REF, bam, INTERVALS_FILE) + " --no_cmdline_in_header -o %s -minPruning 3";
         final WalkerTestSpec spec = new WalkerTestSpec(base + " " + args, Arrays.asList(md5));
         executeTest("testHaplotypeCaller: args=" + args, spec);
     }
@@ -176,7 +177,7 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest {
     }
 
     private void HCTestIndelQualityScores(String bam, String args, String md5) {
-        final String base = String.format("-T HaplotypeCaller --disableDithering --pcr_indel_model NONE -pairHMMSub %s -R %s -I %s", HMM_SUB_IMPLEMENTATION, REF, bam) + " -L 20:10,005,000-10,025,000 --no_cmdline_in_header -o %s -minPruning 2";
+        final String base = String.format("-T HaplotypeCaller --disableDithering --pcr_indel_model NONE -pairHMMSub %s %s -R %s -I %s", HMM_SUB_IMPLEMENTATION, ALWAYS_LOAD_VECTOR_HMM, REF, bam) + " -L 20:10,005,000-10,025,000 --no_cmdline_in_header -o %s -minPruning 2";
         final WalkerTestSpec spec = new WalkerTestSpec(base + " " + args, Arrays.asList(md5));
         executeTest("testHaplotypeCallerIndelQualityScores: args=" + args, spec);
     }
@@ -191,7 +192,7 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest {
             final IndexedFastaSequenceFile fasta = new IndexedFastaSequenceFile(new File(b37KGReference));
             final GenomeLocParser parser = new GenomeLocParser(fasta.getSequenceDictionary());
 
-            final String base = String.format("-T HaplotypeCaller --disableDithering --pcr_indel_model NONE -pairHMMSub %s -R %s -I %s", HMM_SUB_IMPLEMENTATION, REF, bam) + " -L 20:10,001,603-10,001,642 -L 20:10,001,653-10,001,742 --no_cmdline_in_header -o %s";
+            final String base = String.format("-T HaplotypeCaller --disableDithering --pcr_indel_model NONE -pairHMMSub %s %s -R %s -I %s", HMM_SUB_IMPLEMENTATION, ALWAYS_LOAD_VECTOR_HMM, REF, bam) + " -L 20:10,001,603-10,001,642 -L 20:10,001,653-10,001,742 --no_cmdline_in_header -o %s";
             final WalkerTestSpec spec = new WalkerTestSpec(base + " " + args, Arrays.asList(md5));
             for( final File vcf : executeTest("testHaplotypeCallerNearbySmallIntervals: args=" + args, spec).getFirst() ) {
                 if( containsDuplicateRecord(vcf, parser) ) {
@@ -229,14 +230,14 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest {
     // any of the calls in that region because it is so messy.
     @Test
     public void HCTestProblematicReadsModifiedInActiveRegions() {
-        final String base = String.format("-T HaplotypeCaller --disableDithering --pcr_indel_model NONE -pairHMMSub %s -R %s -I %s", HMM_SUB_IMPLEMENTATION, REF, privateTestDir + "haplotype-problem-4.bam") + " --no_cmdline_in_header -o %s -minPruning 3 -L 4:49139026-49139965";
+        final String base = String.format("-T HaplotypeCaller --disableDithering --pcr_indel_model NONE -pairHMMSub %s %s -R %s -I %s", HMM_SUB_IMPLEMENTATION, ALWAYS_LOAD_VECTOR_HMM, REF, privateTestDir + "haplotype-problem-4.bam") + " --no_cmdline_in_header -o %s -minPruning 3 -L 4:49139026-49139965";
         final WalkerTestSpec spec = new WalkerTestSpec(base, Arrays.asList("cf6fbb3636c52cd47dd14e0bd415a320"));
         executeTest("HCTestProblematicReadsModifiedInActiveRegions: ", spec);
     }
 
     @Test
     public void HCTestStructuralIndels() {
-        final String base = String.format("-T HaplotypeCaller --disableDithering --pcr_indel_model NONE -pairHMMSub %s -R %s -I %s", HMM_SUB_IMPLEMENTATION, REF, privateTestDir + "AFR.structural.indels.bam") + " --no_cmdline_in_header -o %s -minPruning 6 -L 20:8187565-8187800 -L 20:18670537-18670730";
+        final String base = String.format("-T HaplotypeCaller --disableDithering --pcr_indel_model NONE -pairHMMSub %s %s -R %s -I %s", HMM_SUB_IMPLEMENTATION, ALWAYS_LOAD_VECTOR_HMM, REF, privateTestDir + "AFR.structural.indels.bam") + " --no_cmdline_in_header -o %s -minPruning 6 -L 20:8187565-8187800 -L 20:18670537-18670730";
         final WalkerTestSpec spec = new WalkerTestSpec(base, Arrays.asList("a145c3c0e99b278054a9960923da8aaa"));
         executeTest("HCTestStructuralIndels: ", spec);
     }
@@ -244,14 +245,14 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest {
     @Test
     public void HCTestDoesNotFailOnBadRefBase() {
         // don't care about the output - just want to make sure it doesn't fail
-        final String base = String.format("-T HaplotypeCaller --disableDithering -pairHMMSub %s -R %s -I %s", HMM_SUB_IMPLEMENTATION, REF, privateTestDir + "NA12878.readsOverBadBase.chr3.bam") + " --no_cmdline_in_header -o /dev/null -L 3:60830000-60840000 --minPruning 3 -stand_call_conf 2 -stand_emit_conf 2";
+        final String base = String.format("-T HaplotypeCaller --disableDithering -pairHMMSub %s %s -R %s -I %s", HMM_SUB_IMPLEMENTATION, ALWAYS_LOAD_VECTOR_HMM, REF, privateTestDir + "NA12878.readsOverBadBase.chr3.bam") + " --no_cmdline_in_header -o /dev/null -L 3:60830000-60840000 --minPruning 3 -stand_call_conf 2 -stand_emit_conf 2";
         final WalkerTestSpec spec = new WalkerTestSpec(base, Collections.emptyList());
         executeTest("HCTestDoesNotFailOnBadRefBase: ", spec);
     }
 
     @Test
     public void HCTestDanglingTailMergingForDeletions() throws IOException {
-        final String base = String.format("-T HaplotypeCaller --disableDithering --pcr_indel_model NONE -pairHMMSub %s -R %s -I %s", HMM_SUB_IMPLEMENTATION, REF, NA12878_BAM) + " --no_cmdline_in_header -o %s -L 20:10130740-10130800 --allowNonUniqueKmersInRef";
+        final String base = String.format("-T HaplotypeCaller --disableDithering --pcr_indel_model NONE -pairHMMSub %s %s -R %s -I %s", HMM_SUB_IMPLEMENTATION, ALWAYS_LOAD_VECTOR_HMM, REF, NA12878_BAM) + " --no_cmdline_in_header -o %s -L 20:10130740-10130800 --allowNonUniqueKmersInRef";
         final WalkerTestSpec spec = new WalkerTestSpec(base, 1, Arrays.asList(""));
         final File outputVCF = executeTest("HCTestDanglingTailMergingForDeletions", spec).getFirst().get(0);
 
@@ -275,7 +276,7 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest {
 
     @Test
     public void testLeftAlignmentBamOutBugFix() {
-        final String base = String.format("-T HaplotypeCaller -pairHMMSub %s -R %s -I %s", HMM_SUB_IMPLEMENTATION, REF, LEFT_ALIGNMENT_BAMOUT_TEST_INPUT)
+        final String base = String.format("-T HaplotypeCaller -pairHMMSub %s %s -R %s -I %s", HMM_SUB_IMPLEMENTATION, ALWAYS_LOAD_VECTOR_HMM, REF, LEFT_ALIGNMENT_BAMOUT_TEST_INPUT)
                 + " --no_cmdline_in_header -bamout %s -o /dev/null -L 1:11740000-11740700 --allowNonUniqueKmersInRef";
         final WalkerTestSpec spec = new WalkerTestSpec(base, 1, Arrays.asList("c19f0e62f90794661f5927c360d50998"));
         executeTest("LeftAlignmentBamOutBugFix", spec);
@@ -291,7 +292,7 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest {
     @Test
     public void HCTestDBSNPAnnotationWGS() {
         WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
-                "-T HaplotypeCaller --disableDithering --pcr_indel_model NONE -pairHMMSub " + HMM_SUB_IMPLEMENTATION + " -R " + b37KGReference + " --no_cmdline_in_header -I " + NA12878_PCRFREE + " -o %s -L 20:10,090,000-10,100,000 -D " + b37dbSNP132, 1,
+                "-T HaplotypeCaller --disableDithering --pcr_indel_model NONE -pairHMMSub " +  HMM_SUB_IMPLEMENTATION + " " + ALWAYS_LOAD_VECTOR_HMM + " -R " + b37KGReference + " --no_cmdline_in_header -I " + NA12878_PCRFREE + " -o %s -L 20:10,090,000-10,100,000 -D " + b37dbSNP132, 1,
                 Arrays.asList("f0618b66e088b2d6fd831bb357de933c"));
         executeTest("HC calling with dbSNP ID annotation on WGS intervals", spec);
     }
@@ -299,7 +300,7 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest {
     @Test
     public void HCTestDBSNPAnnotationWEx() {
         WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
-                "-T HaplotypeCaller --disableDithering --pcr_indel_model NONE -pairHMMSub " + HMM_SUB_IMPLEMENTATION + " -R " + b37KGReference + " --no_cmdline_in_header -I " + NA12878_PCRFREE + " -o %s -L 20:10,100,000-11,000,000 -D " + b37dbSNP132
+                "-T HaplotypeCaller --disableDithering --pcr_indel_model NONE -pairHMMSub " +  HMM_SUB_IMPLEMENTATION + " " + ALWAYS_LOAD_VECTOR_HMM + " -R " + b37KGReference + " --no_cmdline_in_header -I " + NA12878_PCRFREE + " -o %s -L 20:10,100,000-11,000,000 -D " + b37dbSNP132
                         + " -L " + hg19Intervals + " -isr INTERSECTION", 1,
                 Arrays.asList("b279dfa0864495d0cbe45167c13d5a75"));
         executeTest("HC calling with dbSNP ID annotation on WEx intervals", spec);
@@ -308,7 +309,7 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest {
     @Test
     public void HCTestDBSNPAnnotationWGSGraphBased() {
         WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
-                "-T HaplotypeCaller -likelihoodEngine GraphBased --disableDithering --pcr_indel_model NONE -pairHMMSub " + HMM_SUB_IMPLEMENTATION + " -R " + b37KGReference + " --no_cmdline_in_header -I " + NA12878_PCRFREE + " -o %s -L 20:10,090,000-10,100,000 -D " + b37dbSNP132, 1,
+                "-T HaplotypeCaller -likelihoodEngine GraphBased --disableDithering --pcr_indel_model NONE -pairHMMSub " +  HMM_SUB_IMPLEMENTATION + " " + ALWAYS_LOAD_VECTOR_HMM + " -R " + b37KGReference + " --no_cmdline_in_header -I " + NA12878_PCRFREE + " -o %s -L 20:10,090,000-10,100,000 -D " + b37dbSNP132, 1,
                 Arrays.asList("1b15b696671a9da000d5ec0372f939a2"));
         executeTest("HC calling with dbSNP ID annotation on WGS intervals", spec);
     }
@@ -316,7 +317,7 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest {
     @Test
     public void HCTestDBSNPAnnotationWExGraphBased() {
         WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
-                "-T HaplotypeCaller -likelihoodEngine GraphBased --disableDithering --pcr_indel_model NONE -pairHMMSub " + HMM_SUB_IMPLEMENTATION + " -R " + b37KGReference + " --no_cmdline_in_header -I " + NA12878_PCRFREE + " -o %s -L 20:10,000,000-11,000,000 -D " + b37dbSNP132
+                "-T HaplotypeCaller -likelihoodEngine GraphBased --disableDithering --pcr_indel_model NONE -pairHMMSub " +  HMM_SUB_IMPLEMENTATION + " " + ALWAYS_LOAD_VECTOR_HMM + " -R " + b37KGReference + " --no_cmdline_in_header -I " + NA12878_PCRFREE + " -o %s -L 20:10,000,000-11,000,000 -D " + b37dbSNP132
                         + " -L " + hg19Intervals + " -isr INTERSECTION", 1,
                 Arrays.asList("e46d99fb778e2aff09ccbbc1bda2a1bf"));
         executeTest("HC calling with dbSNP ID annotation on WEx intervals", spec);
@@ -325,7 +326,7 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest {
     @Test
     public void HCTestGraphBasedPCRFreePositiveLogLkFix() {
         WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
-                "-T HaplotypeCaller -likelihoodEngine GraphBased --disableDithering --pcr_indel_model NONE -pairHMMSub " + HMM_SUB_IMPLEMENTATION + " -R " + hg19Reference + " --no_cmdline_in_header -I " + NA12878_PCRFREE250_ADAPTER_TRIMMED + " -o %s -L 20:10,024,000-10,024,500 "
+                "-T HaplotypeCaller -likelihoodEngine GraphBased --disableDithering --pcr_indel_model NONE -pairHMMSub " +  HMM_SUB_IMPLEMENTATION + " " + ALWAYS_LOAD_VECTOR_HMM + " -R " + hg19Reference + " --no_cmdline_in_header -I " + NA12878_PCRFREE250_ADAPTER_TRIMMED + " -o %s -L 20:10,024,000-10,024,500 "
                         , 1,
                 Arrays.asList(""));
         executeTest("HCTestGraphBasedPCRFreePositiveLogLkFix", spec);
@@ -340,24 +341,24 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest {
     @Test
     public void HCTestAggressivePcrIndelModelWGS() {
         WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
-                "-T HaplotypeCaller --disableDithering --pcr_indel_model AGGRESSIVE -pairHMMSub " + HMM_SUB_IMPLEMENTATION + " -R " + b37KGReference + " --no_cmdline_in_header -I " + NA12878_BAM + " -o %s -L 20:10,270,000-10,300,000", 1,
-                Arrays.asList("163a42e1144be1dc905233a8a42b72f6"));
+                "-T HaplotypeCaller --disableDithering --pcr_indel_model AGGRESSIVE -pairHMMSub " + HMM_SUB_IMPLEMENTATION +  " " + ALWAYS_LOAD_VECTOR_HMM + " -R " + b37KGReference + " --no_cmdline_in_header -I " + NA12878_BAM + " -o %s -L 20:10,270,000-10,300,000", 1,
+                Arrays.asList("32deea51cad0424bd8517fab3ad264ea"));
         executeTest("HC calling with aggressive indel error modeling on WGS intervals", spec);
     }
 
     @Test
     public void HCTestConservativePcrIndelModelWGS() {
         WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
-                "-T HaplotypeCaller --disableDithering --pcr_indel_model CONSERVATIVE -pairHMMSub " + HMM_SUB_IMPLEMENTATION + " -R " + b37KGReference + " --no_cmdline_in_header -I " + NA12878_BAM + " -o %s -L 20:10,270,000-10,300,000", 1,
-                Arrays.asList("13298981348351e79a2ff5407f206c1d"));
+                "-T HaplotypeCaller --disableDithering --pcr_indel_model CONSERVATIVE -pairHMMSub " + HMM_SUB_IMPLEMENTATION +  " " + ALWAYS_LOAD_VECTOR_HMM  + " -R " + b37KGReference + " --no_cmdline_in_header -I " + NA12878_BAM + " -o %s -L 20:10,270,000-10,300,000", 1,
+                Arrays.asList("04863dcc6f924b294814c9ef05d79a87"));
         executeTest("HC calling with conservative indel error modeling on WGS intervals", spec);
     }
 
     @Test
     public void testNoSuchEdgeBugFix() {
-        final String commandLine = String.format("-T HaplotypeCaller --pcr_indel_model NONE -pairHMMSub %s -R %s -I %s -L %s -dontTrimActiveRegions -ERC GVCF " +
+        final String commandLine = String.format("-T HaplotypeCaller --pcr_indel_model NONE -pairHMMSub %s %s -R %s -I %s -L %s -dontTrimActiveRegions -ERC GVCF " +
                 "-likelihoodEngine GraphBased -variant_index_type %s -variant_index_parameter %d",
-                HMM_SUB_IMPLEMENTATION, b37KGReferenceWithDecoy, privateTestDir + "graphbased_no_such_edge_bug.bam", privateTestDir + "graphbased_no_such_edge_bug.intervals.bed",
+                HMM_SUB_IMPLEMENTATION, ALWAYS_LOAD_VECTOR_HMM, b37KGReferenceWithDecoy, privateTestDir + "graphbased_no_such_edge_bug.bam", privateTestDir + "graphbased_no_such_edge_bug.intervals.bed",
                 HaplotypeCaller.OPTIMAL_GVCF_INDEX_TYPE, HaplotypeCaller.OPTIMAL_GVCF_INDEX_PARAMETER);
         final WalkerTestSpec spec = new WalkerTestSpec(commandLine + " -o %s", Arrays.asList(""));
         spec.disableShadowBCF();
@@ -367,8 +368,8 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest {
     // This test takes longer than 15 secs ... ~ 25-35 ,
     @Test
     public void testLackSensitivityDueToBadHaplotypeSelectionFix() {
-        final String commandLine = String.format("-T HaplotypeCaller -pairHMMSub %s -R %s -I %s -L %s --no_cmdline_in_header --maxNumHaplotypesInPopulation 16",
-                HMM_SUB_IMPLEMENTATION, b37KGReferenceWithDecoy, privateTestDir + "hc-lack-sensitivity.bam", privateTestDir + "hc-lack-sensitivity.interval_list");
+        final String commandLine = String.format("-T HaplotypeCaller -pairHMMSub %s %s -R %s -I %s -L %s --no_cmdline_in_header --maxNumHaplotypesInPopulation 16",
+                HMM_SUB_IMPLEMENTATION, ALWAYS_LOAD_VECTOR_HMM, b37KGReferenceWithDecoy, privateTestDir + "hc-lack-sensitivity.bam", privateTestDir + "hc-lack-sensitivity.interval_list");
         final WalkerTestSpec spec = new WalkerTestSpec(commandLine + " -o %s", Arrays.asList("9fa83f82ba63729edd8696e82bfeea49"));
         spec.disableShadowBCF();
         executeTest("testLackSensitivityDueToBadHaplotypeSelectionFix", spec);
@@ -376,8 +377,8 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest {
 
     @Test
     public void testMissingKeyAlternativeHaplotypesBugFix() {
-        final String commandLine = String.format("-T HaplotypeCaller -pairHMMSub %s -R %s -I %s -L %s --no_cmdline_in_header ",
-                HMM_SUB_IMPLEMENTATION, b37KGReferenceWithDecoy, privateTestDir + "lost-alt-key-hap.bam", privateTestDir + "lost-alt-key-hap.interval_list");
+        final String commandLine = String.format("-T HaplotypeCaller -pairHMMSub %s %s -R %s -I %s -L %s --no_cmdline_in_header ",
+                HMM_SUB_IMPLEMENTATION, ALWAYS_LOAD_VECTOR_HMM, b37KGReferenceWithDecoy, privateTestDir + "lost-alt-key-hap.bam", privateTestDir + "lost-alt-key-hap.interval_list");
         final WalkerTestSpec spec = new WalkerTestSpec(commandLine + " -o %s", Arrays.asList("423b70c151a5d0028e104aa3372b8783"));
         spec.disableShadowBCF();
         executeTest("testMissingKeyAlternativeHaplotypesBugFix", spec);
@@ -390,9 +391,9 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest {
         final String TEST_BAM = privateTestDir + "sw_epsilon_test.bam";
         final String REFERENCE = b37KGReference;
         final String DBSNP = b37dbSNP138;
-        final String commandLineWithoutInterval = String.format("-T HaplotypeCaller -pairHMMSub %s -I %s -R %s -D %s "
+        final String commandLineWithoutInterval = String.format("-T HaplotypeCaller -pairHMMSub %s %s -I %s -R %s -D %s "
                 + "-variant_index_type  LINEAR -variant_index_parameter 128000 --no_cmdline_in_header "
-                + "-stand_call_conf 10.0 -stand_emit_conf 10.0",HMM_SUB_IMPLEMENTATION,TEST_BAM,REFERENCE,DBSNP);
+                + "-stand_call_conf 10.0 -stand_emit_conf 10.0", HMM_SUB_IMPLEMENTATION, ALWAYS_LOAD_VECTOR_HMM, TEST_BAM, REFERENCE, DBSNP);
 
         final String commandLineShortInterval = commandLineWithoutInterval + " -L " + SHORT_INTERVAL;
         final String commandLineLongInterval = commandLineWithoutInterval + " -L " + LONG_INTERVAL;
@@ -415,7 +416,8 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest {
                         " -T HaplotypeCaller" +
                                 " --contamination_fraction_to_filter 0.05 --disableDithering --pcr_indel_model NONE --maxReadsInRegionPerSample 1000 " +
                                 " --minReadsPerAlignmentStart 5 --maxProbPropagationDistance 50 --activeProbabilityThreshold 0.002 " +
-                                " --no_cmdline_in_header -minPruning 3 -pairHMM VECTOR_LOGLESS_CACHING -pairHMMSub TEST_BEYOND_CAPABILITIES" +
+                                " --no_cmdline_in_header -minPruning 3 -pairHMM VECTOR_LOGLESS_CACHING -pairHMMSub TEST_BEYOND_CAPABILITIES " +
+                                ALWAYS_LOAD_VECTOR_HMM +
                                 " -R " + REF +
                                 " -I " + NA12878_BAM +
                                 " -L " + INTERVALS_FILE +
diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeCallerModesIntegrationTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeCallerModesIntegrationTest.java
index 5c1c8a000..f5894b84f 100644
--- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeCallerModesIntegrationTest.java
+++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeCallerModesIntegrationTest.java
@@ -71,6 +71,7 @@ public class HaplotypeCallerModesIntegrationTest extends WalkerTest {
     // --------------------------------------------------------------------------------------------------------------
 
     final static String HMM_SUB_IMPLEMENTATION = "UNVECTORIZED";
+    final static String ALWAYS_LOAD_VECTOR_HMM = "-alwaysloadVectorHMM";
 
     @Test
     public void HCTestBamWriterCalledHaplotypes() {
@@ -84,7 +85,7 @@ public class HaplotypeCallerModesIntegrationTest extends WalkerTest {
 
     public void HCTestBamWriter(final HaplotypeBAMWriter.Type type, final String md5) {
         WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
-                "-T HaplotypeCaller -pairHMMSub " + HMM_SUB_IMPLEMENTATION + " -R " + b37KGReference + " --no_cmdline_in_header -I " + privateTestDir + "PCRFree.2x250.Illumina.20_10_11.bam -o /dev/null " +
+                "-T HaplotypeCaller -pairHMMSub " + HMM_SUB_IMPLEMENTATION + " " + ALWAYS_LOAD_VECTOR_HMM + " -R " + b37KGReference + " --no_cmdline_in_header -I " + privateTestDir + "PCRFree.2x250.Illumina.20_10_11.bam -o /dev/null " +
                         "-bamout %s -L 20:10,000,000-10,010,000 -bamWriterType " + type, 1,
                 Arrays.asList(md5));
         executeTest("HC writing bams with mode " + type, spec);
diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeCallerParallelIntegrationTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeCallerParallelIntegrationTest.java
index 06b1aa3cc..ed3413364 100644
--- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeCallerParallelIntegrationTest.java
+++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeCallerParallelIntegrationTest.java
@@ -62,6 +62,7 @@ import java.util.List;
 public class HaplotypeCallerParallelIntegrationTest extends WalkerTest {
 
     final static String HMM_SUB_IMPLEMENTATION = "UNVECTORIZED";
+    final static String ALWAYS_LOAD_VECTOR_HMM = "-alwaysloadVectorHMM";
 
     @DataProvider(name = "NCTDataProvider")
     public Object[][] makeNCTDataProvider() {
@@ -77,7 +78,7 @@ public class HaplotypeCallerParallelIntegrationTest extends WalkerTest {
     @Test(dataProvider = "NCTDataProvider")
     public void testHCNCT(final int nct, final String md5) {
         WalkerTestSpec spec = new WalkerTestSpec(
-                "-T HaplotypeCaller --pcr_indel_model NONE -pairHMMSub " + HMM_SUB_IMPLEMENTATION + " -R " + b37KGReference + " --no_cmdline_in_header -I "
+                "-T HaplotypeCaller --pcr_indel_model NONE -pairHMMSub " + HMM_SUB_IMPLEMENTATION + " " + ALWAYS_LOAD_VECTOR_HMM + " -R " + b37KGReference + " --no_cmdline_in_header -I "
                         + privateTestDir + "PCRFree.2x250.Illumina.20_10_11.bam -o %s " +
                         " -L 20:10,000,000-10,100,000 -G none -A none -contamination 0.0 -nct " + nct, 1,
                 Arrays.asList(md5));
diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/PairHMMLikelihoodCalculationEngineUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/PairHMMLikelihoodCalculationEngineUnitTest.java
index 84087b76e..40e3aa30e 100644
--- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/PairHMMLikelihoodCalculationEngineUnitTest.java
+++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/PairHMMLikelihoodCalculationEngineUnitTest.java
@@ -138,7 +138,7 @@ public class PairHMMLikelihoodCalculationEngineUnitTest extends BaseTest {
     public void createPcrErrorModelTest(final String repeat, final int repeatLength) {
 
         final PairHMMLikelihoodCalculationEngine engine = new PairHMMLikelihoodCalculationEngine((byte)0,
-                PairHMM.HMM_IMPLEMENTATION.ORIGINAL, PairHMM.HMM_SUB_IMPLEMENTATION.ENABLE_ALL, 0.0, true,
+                PairHMM.HMM_IMPLEMENTATION.ORIGINAL, PairHMM.HMM_SUB_IMPLEMENTATION.UNVECTORIZED, false, 0.0, true,
                 PairHMMLikelihoodCalculationEngine.PCR_ERROR_MODEL.CONSERVATIVE);
 
         final String readString = Utils.dupString(repeat, repeatLength);
diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/ReadThreadingLikelihoodCalculationEngineUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/ReadThreadingLikelihoodCalculationEngineUnitTest.java
index baf48cf31..119cf45fd 100644
--- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/ReadThreadingLikelihoodCalculationEngineUnitTest.java
+++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/ReadThreadingLikelihoodCalculationEngineUnitTest.java
@@ -95,7 +95,7 @@ public class ReadThreadingLikelihoodCalculationEngineUnitTest extends ActiveRegi
     //final PairHMMLikelihoodCalculationEngine fullPairHMM = new PairHMMLikelihoodCalculationEngine((byte)10, false,
     //        PairHMM.HMM_IMPLEMENTATION.LOGLESS_CACHING, -3);
     final PairHMMLikelihoodCalculationEngine fullPairHMM = new PairHMMLikelihoodCalculationEngine((byte)10,
-            PairHMM.HMM_IMPLEMENTATION.LOGLESS_CACHING, PairHMM.HMM_SUB_IMPLEMENTATION.ENABLE_ALL, Double.NEGATIVE_INFINITY,
+            PairHMM.HMM_IMPLEMENTATION.LOGLESS_CACHING, PairHMM.HMM_SUB_IMPLEMENTATION.UNVECTORIZED, true, Double.NEGATIVE_INFINITY,
             true, PairHMMLikelihoodCalculationEngine.PCR_ERROR_MODEL.NONE);
 
     // When using likelihoods it should be around 0.05 since